Spermatogenesis is a tightly regulated process; it is characterized by spermatogonial stem cells undergoing mitotic expansion and differentiation, spermatocytes undergoing meiosis, and spermatids undergoing transformation to spermatozoa. Spermatogonial stem cell maturation and proliferation provides a unique model for studying the factors that control renewal and differentiation. Specific changes occur in the cell population with each step resulting in a more differentiated state. Knowledge of the factors that result in the transition of germ cells down the differentiation pathway will be helpful in enhancing our understanding of the biological changes occur during human differentiation. Techniques are available for isolating relatively pure cell population at specific stages during spermatogenesis. Animal models are also available which permit study of arrest and restart of spermatogonial differentiation. One of the goals of this research is to delineate the genes that regulate spermatogenesis using expression gene profiling techniques including DNA microarrays and serial analysis of gene expression (SAGE). Currently, we are studying gene profiles of three germ cell populations, namely, type A spermatogonia, pachytene spermatocytes, and round spermatids as well as a putative spermatogonial cell line. cDNA microarray analysis using mouse GeneFilters from ResGen with 5,148 cDNA elements has identified 79 cDNAs that can be clustered into 12 changing patterns during spermatogenesis. Among these cDNAs only 12 are known mouse genes, 16 are ESTs with similarity to known genes, and the rest undefined ESTs. The 10 most abundant cDNAs in type A spermatogonia are ESTs. This large number of ESTs reinforces the fact that little is known about the genetic regulation of spermatogenesis and is suggestive of leads for further investigation. Similar results were obtained with SAGE analysis. We have only performed SAGE with pachytene spermatocytes. However, preliminary analysis of 18,500 tags has identified several tags with no match in the mouse SAGEmap database. We will continue to analyze germ cell transcriptomes at different stages of spermatogenesis. We will study the change of the transcriptome of germ cells under different experimental conditions that affect spermatogenesis. The effect of abrogation of some of the selected genes on spermatogenesis will also be studied. Additionally, we plan to generate a SAGE database for mouse germ cell genes within the coming year.